(A) (B) (C) (D) Figure S1. (A) Picture of Ziziphus mauritiana tree -a medium sized tree and leaves are alternate, oblong- ovate, obtuse or acute and nearly asymmetric. (B &C) Flowers are in cymes, pedicellate. Ovary is syncarpous, inferior, 2-4 celled, ovules one per cell and stigma 2-4 lobed. (D) Fruit is drupe, fleshy, yellow or red brown. The ripe fruit is sweet and sour in taste and has single hard, rough stone. Stone contains 1-2 elliptic brown kernels (Pareek, 2001; Jagwan and Singh, 2009).

(A) III I I IIa IIb III IIa IV IIb IV S1R1 S3R33 S7R6 S6R14 S6R8 S7R2 S11R14 S11R10 S4R10 S3R14 S10R16 S3R20 S10R10 S6R17 S5R7 S8R6 S3R6 S4R26 S3R4 S2R22 S9R32 S9R31 S9R30 S10R20 S9R23 S6R27 S5R32 S2R9 S5R5 S4R25 S11R3 S11R2 S5R3 S8R12 S5R21 S3R25 S3R1 S11R1 S10R15 S7R20 S6R29 S3R32 S7R8 S4R28 S5R24 S3R22 S5R23 S8R14 S3R26 S5R18 S10R4 S9R17 S5R6 S10R18 S10R19 S3R11 S2R24 S10R28 S6R28 S1R27 S6R21 S10R29 S6R16 S5R22 S3R3 S1R23 S5R27 S1R15 S2R17 S6R12 S5R4 S3R10 S6R13 S6R6 S6R11 S2R29 S8R13 S8R17 S3R2 S2R27 S10R14 S7R1 S2R20 S10R7 S7R9 S4R22 S8R8 S9R12 S1R8 S6R32 S3R29 S6R30 S6R31 S2R21 S6R22 S6R20 S6R33 S5R33 S5R29 S2R12 S2R2 S2R8 S1R6 S1R9 S5R1 S1R30 S1R16 I S1R5 S1R2 I S1R31 S3R19 S3R30 S1R26 S1R18 S2R10 S2R26 S2R14 S6R10 S6R19 S2R31 S2R25 S1R21 S3R31 IIa S1R7 S2R28 S5R31 S2R33 S4R17 S1R12 S2R11 S1R32 S5R15 IIb S6R7 S2R6 S3R12 S2R15 S4R3 S2R7 S4R16 III S1R19 S2R18 S3R23 IIa IV IIb S11R16 S9R33 S9R27 S7R31 S7R29 S5R19 S10R8 S10R12 S10R30 S6R23 S6R1 S8R2 S6R25 S6R4 S5R16 S10R21 S4R4 S11R6 S10R2 S4R6 S9R8 S11R4 S9R1 S5R11 S3R16 S10R25 S8R10 S7R27 S5R28 S5R30 S5R26 S5R25 S3R18 S3R13 S8R9 S6R3 S2R16 S5R2 S4R13 S2R13 S2R3 S4R29 S4R12 S2R30 S2R1 (A) IV S11R8 S8R15 S7R33 S4R1 S9R24 S10R32 S10R23 S9R15 S7R14 S3R27 S8R4 S7R23 S3R8 S2R4 S4R32 S9R13 S7R12 S7R10 S7R25 S11R12 S9R10 S9R3 S7R4 S4R30 S9R5 S1R28 S10R5 S1R24 S4R18 S1R13 S5R9 S7R18 S4R14 S4R23 S7R21 S8R18 S7R16 S4R8 S1R10 S1R3 III S1R33 S1R22 S2R32 S1R17 S8R27 S8R25 S8R22 S8R20 S5R13 Figure S2 Phylogenetic tree developed for whole collection using phenotypic traits of majority of the Z. mauritiana germplasm accessions by SAS 9.3 software. Roman letters indicate the number of clusters. The each cluster has been expanded for clear view. Bold letters are the accessions belong to the core collection.

Roman letters indicate the number of clusters Average Distance Between Clusters 1.8 1.6 1.4 1.2 1.0 0.8 0.6 0.4 0.2 0.0 S11R7 S9R24 S4R1 S2R4 S8R18 S7R18 S1R24 S2R19 S1R33 S1R22 S2R32 S1R17 S1R16 S10R2 S7R27 S7R6 S4R31 S4R33 S5R19 S11R2 S7R3 S5R3 S3R32 S2R16 S6R21 S3R3 S1R15 S5R31 S2R33 S1R12 S5R6 S2R17 S3R29 S2R2 S4R22 S1R8 S6R12 S2R14 S1R4 S1R2 Figure S3Phylogenetic tree developed for core collection using phenotypic traits of most of the accessions by SAS 9.3 software. Roman letters indicate the number of clusters